X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 10% PEG 20000, 15% glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.55 α = 79.28
b = 64.28 β = 87.38
c = 75.4 γ = 90.2
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Osmic 2009-05-21
Diffraction Radiation
Monochromator Protocol
Multilayer Optic SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.541700 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.3 40 95.8 0.063 -- -- 2.21 11797 11298 -- -3.0 18.547
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.3 3.4 95.6 0.171 -- 5.64 2.2 998

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.3 28.58 -- 0.0 -- 11296 678 100.0 -- 0.193 0.1889 0.2563 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.3 3.385 -- 49 771 0.276 0.407 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.4479
Anisotropic B[1][1] -0.71
Anisotropic B[1][2] -0.22
Anisotropic B[1][3] -0.18
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] 0.54
Anisotropic B[3][3] 0.36
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.707
r_scbond_it 0.941
r_mcangle_it 0.867
r_mcbond_it 0.456
r_gen_planes_refined 0.005
r_chiral_restr 0.08
r_dihedral_angle_4_deg 15.646
r_dihedral_angle_3_deg 19.03
r_dihedral_angle_2_deg 38.328
r_dihedral_angle_1_deg 5.541
r_angle_refined_deg 1.224
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4190
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 1.3.1 molecular replacement
Xscale data reduction